Sun Oct 9 14:46:51 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:46:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5417827 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -20.31200 45.39700 ymin,ymax (A): -22.90100 28.24800 zmin,zma (A): -9.926000 37.43500 x,y,z range (A): 65.70900 51.14900 47.36100 scale (grids/A): 0.5417827 object centre (A): 12.54250 2.673501 13.75450 number of atom coordinates read : 2595 total number of charged atoms : 2454 net assigned charge : 4.000017 assigned positive charge : 388.4748 centred at (gu) : 89.79041 89.66122 90.21964 assigned negative charge : -384.4754 centred at (gu) : 89.57156 89.73836 90.11641 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5021 nv = 96 ne = 84 npr = 49881 no. pairs analyzed = 49881 no. exposed pairs = 3695 no. arc points = 26735 no. surface atoms = 1229 nbur = 1366 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 196 mr = 2255 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8393693E-10 7.5332146E-10 midg,1,midg; midg,igrid,midg 6.3972994E-10 -1.5495392E-10 1,midg,midg; igrid,midg,midg -9.4156583E-10 1.1935356E-09 gauss-seidel spectral radius is 0.9824196 estimated iterations to convergence 62 setup time was (sec) 0.4900000 now iterating at: 14:46:51 rms-change max change #iterations 6.2723219E-02 12.25286 at 10iterations 4.0919087E-03 0.8219147 at 20iterations 2.6986789E-04 4.8718691E-02 at 30iterations 2.0018886E-05 3.5400391E-03 at 40iterations 2.1228389E-06 3.1280518E-04 at 50iterations finished qdiffx linear iterations at : 14:46:54 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 2.1228389E-06 3.1280518E-04 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:46:54 3.071u 0.150s 0:03.49 92.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:46:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.625348 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -20.31200 45.39700 ymin,ymax (A): -22.90100 28.24800 zmin,zma (A): -9.926000 37.43500 x,y,z range (A): 65.70900 51.14900 47.36100 scale (grids/A): 1.625348 object centre (A): 12.54250 2.673501 13.75450 number of atom coordinates read : 2595 total number of charged atoms : 2454 net assigned charge : 4.000017 assigned positive charge : 388.4748 centred at (gu) : 89.37045 88.98314 90.65847 assigned negative charge : -384.4754 centred at (gu) : 88.71431 89.21462 90.34906 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 55473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26735 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15380 mr = 34715 m= 1396 mr = 9503 m= 37 mr = 491 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 27575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18792 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5417827 object centre at (A) : 12.54250 2.673501 13.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1755175E-03 6.2184855E-03 midg,1,midg; midg,igrid,midg 2.8622526E-04 -4.1810172E-03 1,midg,midg; igrid,midg,midg -4.0222771E-02 1.8980345E-02 gauss-seidel spectral radius is 0.9981420 estimated iterations to convergence 184 setup time was (sec) 0.6600000 now iterating at: 14:46:55 rms-change max change #iterations 3.013274 155.8621 at 10iterations 1.235085 58.33611 at 20iterations 0.5067666 23.53606 at 30iterations 0.2071783 8.323257 at 40iterations 8.5518144E-02 3.236835 at 50iterations 3.5203535E-02 1.476857 at 60iterations 1.4494413E-02 0.5769238 at 70iterations 5.9554894E-03 0.2393384 at 80iterations 2.4686146E-03 0.1010056 at 90iterations 1.0118661E-03 4.0936947E-02 at 100iterations 4.1725644E-04 1.5546799E-02 at 110iterations 1.7258988E-04 6.6628456E-03 at 120iterations finished qdiffx linear iterations at : 14:47:01 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 1.7258988E-04 6.6628456E-03 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 14:47:01 6.730u 0.141s 0:07.18 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:47:01 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.438022 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -20.31200 45.39700 ymin,ymax (A): -22.90100 28.24800 zmin,zma (A): -9.926000 37.43500 x,y,z range (A): 65.70900 51.14900 47.36100 scale (grids/A): 2.438022 object centre (A): 12.54250 2.673501 13.75450 number of atom coordinates read : 2595 total number of charged atoms : 2454 net assigned charge : 4.000017 assigned positive charge : 388.4748 centred at (gu) : 89.05546 88.47455 90.98756 assigned negative charge : -384.4754 centred at (gu) : 88.07146 88.82189 90.52354 start vw surface at 0.1500000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 128860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26735 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 54086 mr = 85923 m= 13745 mr = 40372 m= 1958 mr = 9254 m= 113 mr = 1045 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 62143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19602 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.625348 object centre at (A) : 12.54250 2.673501 13.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4551300E-02 8.1965826E-02 midg,1,midg; midg,igrid,midg -1.6780786E-02 -5.1699903E-02 1,midg,midg; igrid,midg,midg -0.6686409 0.1924918 gauss-seidel spectral radius is 0.9991229 estimated iterations to convergence 267 setup time was (sec) 1.200000 now iterating at: 14:47:03 rms-change max change #iterations 8.020708 350.4698 at 10iterations 4.535881 197.5094 at 20iterations 2.548224 64.72546 at 30iterations 1.416252 34.39716 at 40iterations 0.7878125 21.09815 at 50iterations 0.4349132 11.13889 at 60iterations 0.2399062 6.646595 at 70iterations 0.1314745 3.101278 at 80iterations 7.2505586E-02 1.664993 at 90iterations 3.9659802E-02 0.9734459 at 100iterations 2.1709939E-02 0.4727011 at 110iterations 1.1877457E-02 0.2740002 at 120iterations 6.5062200E-03 0.1486282 at 130iterations 3.5541879E-03 7.8656077E-02 at 140iterations 1.9423229E-03 4.0763855E-02 at 150iterations 1.0616820E-03 2.8417110E-02 at 160iterations 5.7944597E-04 1.3574481E-02 at 170iterations 3.1685331E-04 7.7896118E-03 at 180iterations finished qdiffx linear iterations at : 14:47:12 total time elapsed so far: 10.38000 # loops : 180 mean,max change (kT/e) : 3.1685331E-04 7.7896118E-03 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 14:47:12 10.563u 0.154s 0:10.99 97.4% 0+0k 0+0io 0pf+0w